Hi Sergio,
I was having errors like that up until I found my working combination of
cmake, boost, and swig (again for CentOS 6.x). A former colleague of mine
also struggled to build the wrappers until he switched to those exact
versions I enumerated earlier.
I wish that I had a more descriptive answer, but I simply tried combination
after combination of those three applications until I found one that
worked.
Let me know if upgrading your version of boost helps!
Matt
On Thu, Jun 5, 2014 at 3:29 PM, Wong, Sergio E. <[email protected]> wrote:
> Hi;
>
> So I switched down to swig 2.0, up to boost 1.47 and up to cmake v.2.8
> and got further, but now have other errors :
>
> ....
>
> [ 98%] Built target GraphMolWrap
> Scanning dependencies of target BuildJavaWrapperTests
> [ 98%] jar cf org.RDKitDoc.jar -d doc
> ----------
> 1. ERROR in src/org/RDKit/AtomColors.java (at line 11)
> public enum AtomColors {
> ^^^^
> Syntax error on token "enum", interface expected
> ----------
>
> ....
>
> 162. ERROR in src/org/RDKit/SanitizeFlags.java (at line 22)
> SANITIZE_ADJUSTHS(RDKFuncsJNI.SANITIZE_ADJUSTHS_get()),
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Syntax error on token(s), misplaced construct(s)
> ----------
> 163. ERROR in src/org/RDKit/SanitizeFlags.java (at line 22)
> SANITIZE_ADJUSTHS(RDKFuncsJNI.SANITIZE_ADJUSTHS_get()),
> ^
> Syntax error, insert ";" to complete InvalidConstructorDeclaration
> ----------
> 164. ERROR in src/org/RDKit/SanitizeFlags.java (at line 23)
> SANITIZE_ALL(RDKFuncsJNI.SANITIZE_ALL_get());
> ^^^^^^^^^^^^^^^^^^^^^^^^^
> Syntax error on token(s), misplaced construct(s)
> ----------
> 165. ERROR in src/org/RDKit/SanitizeFlags.java (at line 23)
> SANITIZE_ALL(RDKFuncsJNI.SANITIZE_ALL_get());
> ^
> Syntax error on token ")", delete this token
> ----------
> 166. ERROR in src/org/RDKit/SanitizeFlags.java (at line 39)
> @SuppressWarnings("unused")
> ^^^^^^^^^^^^^^^^^
> Syntax error, annotations are only available if source level is 5.0
> ----------
> 167. ERROR in src/org/RDKit/SanitizeFlags.java (at line 44)
> @SuppressWarnings("unused")
> ^^^^^^^^^^^^^^^^^
> Syntax error, annotations are only available if source level is 5.0
> ----------
> 168. ERROR in src/org/RDKit/SanitizeFlags.java (at line 50)
> @SuppressWarnings("unused")
> ^^^^^^^^^^^^^^^^^
> Syntax error, annotations are only available if source level is 5.0
> ----------
> 169. ERROR in src/org/RDKit/SanitizeFlags.java (at line 58)
> private static class SwigNext {
> ^^^^^^^^
> The type SwigNext is already defined
> ----------
> 169 problems (163 errors, 6 warnings)make[2]: ***
> [../Code/JavaWrappers/gmwrapper/org.RDKit.jar] Error 255
> make[1]: ***
> [Code/JavaWrappers/gmwrapper/CMakeFiles/BuildJavaWrapperTests.dir/all]
> Error 2
>
> make: *** [all] Error 2
>
>
> Any ideas?
>
> Thanks!
> -Sergio
> ------------------------------
> *From:* Matthew Lardy [[email protected]]
> *Sent:* Thursday, June 05, 2014 1:58 PM
> *To:* Wong, Sergio E.
> *Cc:* [email protected]
> *Subject:* Re: [Rdkit-discuss] installation problem
>
> Hi Sergio,
>
> What version of Swig, Boost and Cmake are you using? I found that
> switching to Swig (v2.0.10), Boost (v1.55), and Cmake (v 2.8.10.2) resolved
> those types of errors when I was having them.
>
> At least that worked on CentOS 6.x. :)
> Matt
>
>
>
> On Thu, Jun 5, 2014 at 1:09 PM, Wong, Sergio E. <[email protected]> wrote:
>
>> Hi;
>>
>> I am trying to install the CDKit, and in particular, the python
>> wrapper on a redhat x86_64 desktop from source. The cmake command I used
>> is:
>>
>> cmake -DBOOST_ROOT=/home/wong105/usr/boost_1_47_0 -D
>> PYTHON_LIBRARY=/usr/lib64/python2.4/config/libpython2.4.a -D
>> PYTHON_INCLUDE_DIR=/usr/include/python2.4 -D
>> PYTHON_EXECUTABLE=/usr/bin/python2.4 -D RDK_BUILD_SWIG_WRAPPERS=ON -D
>> PYTHON_NUMPY_INCLUDE_PATH=/usr/lib64/python2.4/site-packages/numpy/core/include
>> -D SWIG_DIR=/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/ -D
>> SWIG_EXECUTABLE=/home/wong105/usr/swig-3.0.2/bin/swig ../
>>
>> and at the very end, the following set of warnings/errors occur:
>>
>> [ 97%] Built target rdChemicalFeatures
>> [ 97%] Swig source
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:67:
>> Warning 302: Identifier 'int64_t' redefined (ignored),
>> /home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:21: Warning 302:
>> previous definition of 'int64_t'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:68:
>> Warning 302: Identifier 'uint64_t' redefined (ignored),
>> /home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:31: Warning 302:
>> previous definition of 'uint64_t'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:69:
>> Warning 302: Identifier 'int_least64_t' redefined (ignored),
>> /home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:44: Warning 302:
>> previous definition of 'int_least64_t'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:70:
>> Warning 302: Identifier 'uint_least64_t' redefined (ignored),
>> /home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:54: Warning 302:
>> previous definition of 'uint_least64_t'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:71:
>> Warning 302: Identifier 'int_fast64_t' redefined (ignored),
>> /home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:67: Warning 302:
>> previous definition of 'int_fast64_t'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:72:
>> Warning 302: Identifier 'uint_fast64_t' redefined (ignored),
>> /home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:79: Warning 302:
>> previous definition of 'uint_fast64_t'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:73:
>> Warning 302: Identifier 'intmax_t' redefined (ignored),
>> /home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:99: Warning 302:
>> previous definition of 'intmax_t'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:74:
>> Warning 302: Identifier 'uintmax_t' redefined (ignored),
>> /home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:100: Warning 302:
>> previous definition of 'uintmax_t'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/../BitOps.i:47:
>> Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed
>> from 'AllProbeBitsMatch< ExplicitBitVect >'),
>> /home/wong105/usr/RDKit/Code/DataStructs/BitOps.h:72: Warning 302:
>> previous definition of 'AllProbeBitsMatch'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/../BitOps.i:48:
>> Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed
>> from 'AllProbeBitsMatch< ExplicitBitVect >'),
>> /home/wong105/usr/RDKit/Code/DataStructs/BitOps.h:72: Warning 302:
>> previous definition of 'AllProbeBitsMatch'.
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/../BitOps.i:60:
>> Warning 302: Identifier 'NumBitsInCommon' redefined (ignored) (Renamed from
>> 'NumBitsInCommon< ExplicitBitVect,ExplicitBitVect >'),
>> /home/wong105/usr/RDKit/Code/DataStructs/BitOps.h:219: Warning 302:
>> previous definition of 'NumBitsInCommon'.
>> /home/wong105/usr/RDKit/Code/RDBoost/Exceptions.h:18: Warning 401:
>> Nothing known about base class 'std::runtime_error'. Ignored.
>> /home/wong105/usr/RDKit/Code/RDBoost/Exceptions.h:31: Warning 401:
>> Nothing known about base class 'std::runtime_error'. Ignored.
>> /home/wong105/usr/RDKit/Code/RDBoost/Exceptions.h:46: Warning 401:
>> Nothing known about base class 'std::runtime_error'. Ignored.
>> /home/wong105/usr/RDKit/Code/GraphMol/QueryOps.h:347: Warning 401:
>> Nothing known about base class 'Queries::EqualityQuery<
>> int,ConstAtomPtr,true >'. Ignored.
>> /home/wong105/usr/RDKit/Code/GraphMol/QueryOps.h:347: Warning 401: Maybe
>> you forgot to instantiate 'Queries::EqualityQuery< int,ConstAtomPtr,true >'
>> using %template.
>> /home/wong105/usr/RDKit/Code/GraphMol/QueryOps.h:387: Warning 401:
>> Nothing known about base class 'Queries::SetQuery< int,Atom const *,true
>> >'. Ignored.
>> /home/wong105/usr/RDKit/Code/GraphMol/QueryOps.h:387: Warning 401: Maybe
>> you forgot to instantiate 'Queries::SetQuery< int,Atom const *,true >'
>> using %template.
>> /home/wong105/usr/RDKit/Code/GraphMol/SanitException.h:26: Warning 520:
>> Base class 'std::exception' of 'MolSanitizeException' is not similarly
>> marked as a smart pointer.
>> /home/wong105/usr/RDKit/Code/GraphMol/SmilesParse/SmilesParse.h:58:
>> Warning 520: Base class 'std::exception' of 'SmilesParseException' is not
>> similarly marked as a smart pointer.
>> /home/wong105/usr/RDKit/Code/RDGeneral/versions.h:8: Warning 451: Setting
>> a const char * variable may leak memory.
>> /home/wong105/usr/RDKit/Code/RDGeneral/versions.h:13: Warning 451:
>> Setting a const char * variable may leak memory.
>> Unable to open file
>> /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/src/org/RDKit/SWIGTYPE_p_std__pairT_boost__adjacency_listT_boost__vecS_boost__vecS_boost__undirectedS_boost__shared_ptrT_RDKit__Atom_t_boost__shared_ptrT_RDKit__Bond_t_t__adjacency_iterator_boost__adjacency_listT_boost__vecS_boost__vecS_boost__undirectedS_boost__shared_ptrT_RDKit__Atom_t_boost__shared_ptrT_RDKit__Bond_t_t__adjacency_iterator_t.java:
>> File name too long
>> make[2]: *** [Code/JavaWrappers/gmwrapper/GraphMolJavaJAVA_wrap.cxx]
>> Error 1
>> make[1]: ***
>> [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/all] Error 2
>> make: *** [all] Error 2
>>
>> Any ideas on what I may be doing wrong?
>>
>> Thanks!
>> -Sergio
>>
>>
>> ------------------------------------------------------------------------------
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph databases and their
>> applications. Written by three acclaimed leaders in the field,
>> this first edition is now available. Download your free book today!
>> http://p.sf.net/sfu/NeoTech
>> _______________________________________________
>> Rdkit-discuss mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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